Just my vision

1. PHP is excellent and the another... I'd have to go with Java.

2.You should compare how easy it is to create professional looking web pages (at least with my pages Java is better). Other thing you should compare is how can you create functionality for the pages. (PHP rules!)

3. I think you should create a site that has lot's of "real" functions. I create web applications which control industrial processes and that's fun... Just an idea: Web application that controls an automated process (for example car factory or whatever product)

This is all just my vision... I hope this helps you!

I had a similar course in university last fall and showing my web application got me this summer job.

2. I think what the university is looking for here is an actual comparison of the languages, constructs etc. So what I need is more ideas on what I should compare between the languages themselves. (This is the *core* of the project).

3. The three-tier web application is not the *core* of the project but the output produced from the comparions of the two scripting languages.

Thanks for the help and I hope some other guys/gals can give me some input too!

I think that, for a three tier app, you should consider java in all aspects (jsp, beans .....) because they play different roles (and here you can find excellent tutorials).
The challenger, in my opinion is MS with their .net architecture.
Honestly I don't see php a viable option for a real enterprise level multities app.
Good work!